tools in bioinformatics genome browsers. retrieving genomic information previous lesson(s):...

Tools in Bioinformatics

Genome Browsers

Retrieving genomic information

Previous lesson(s): annotation-based perspective of search/data

Today: genomic-based perspective: look at all the data from the prism of a specific chromosome location

Next: sequence-based searches

Genome browsers

NCBI Map Viewer http://www.ncbi.nih.gov/mapview

Ensembl http://www.ensembl.org/

UCSC Genome Browser http://genome.ucsc.edu/

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The UCSC Genome BrowserIntroduction

Materials prepared byMary Mangan, Ph.D.www.openhelix.com

Updated: Q1 2009


UCSC Genome Browser Agenda

UCSC Genome Browser: http://genome.ucsc.edu

Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) Summary Exercises

Introduction and Credits


Organization of Genomic Data

Genome backbone: base position numbersequenceA

nnot

atio

n T

rack

s

chromosome band

known genes

predicted genes

evolutionary conservation

SNPs

sts sites

gap locations

repeated regions

microarray/expression data

more…

Links out to more data


A Sample of the UCSC Genome Browser

gene details

An

nota

tion

Tra

cks

officialsequence

comparisons

SNPs


The UCSC Homepage: http://genome.ucsc.edu

navigate

navigate General information

Specific information—new features, current status, etc.


Genome Browser Gateway: start page, basic search

text/ID searches

Helpful search examples

samples provided

Use this Gateway to search by: Gene names, symbols, IDs Chromosome number: chr7, or region: chr11:1038475-1075482 Keywords: kinase, receptor

See lower part of page for help with format


The Genome Browser Gateway

Make your Gateway choices:

1. Select Clade

2. Select genome = species: search 1 species at a time

3. Assembly: the official backbone DNA sequence

4. Position: location in the genome to examine

5. Image width: how many pixels in display window; 5000 max

6. Configure: make fonts bigger + other choices

4 51 32

assembly

6


The Genome Browser Gatewaysample search for Human TP53

Sample search: human, March 2006 assembly, tp53

select

Select from results list ID search may go right to a viewer page, if unique


Overview of the WholeGenome Browser Page

(mature release)} Genome viewer section

mRNA and EST Tracks

Expression (such as microarray)

Comparative Genomics•As a group•Individual species

Variation and Repeats(including SNPs, copy number variation)

Groups of data (Tracks)Mapping and Sequencing Tracks

Genes and Gene Prediction Tracks(including sno/miRNA data)

ENCODE Tracks

Phenotype and Disease Tracks

Regulation (including TFBS)


Different Species, Different Tracks, Same Software

Species may have different data tracks Layout, software, functions the same


Sample Genome Viewer Image, TP53 Region

base position

UCSC genes

RefSeq genes

mRNAs & ESTs

repeats

many species compared

SNPs

single species compared

MGC clones


Visual Cues on the Genome Browser

Track colors may have meaning—for example, UCSC Gene track:

•If there is a corresponding PDB entry = black•If there is a corresponding reviewed/validated seq = dark blue•If there is a non-RefSeq seq = lightest blue

Tick marks; a single location (STS, SNP)

For some tracks, the height of a bar is increased likelihoodof an evolutionary relationship (conservation track)

Intron and direction of transcription <<< or >>>

<exon exon exon< < < < < < <ex 5' UTR3' UTR

Alignment indications (Conservation pairs: “chain” or “net” style)•Alignments = boxes, Gaps = lines


Options for Changing Images: Upper Section

Change your view or location with controls at the top Use “base” to get right down to the nucleotides Configure: to change font, window size, more…

Next item, next exon navigation assistance can be turned on

Specifya

position

Fonts,window,

next item,more

Walkleft orright

Zoomin

Zoomout

Click tozoom 3x

and re-center


Annotation Track Display Options

Some data is ON or OFF by default

Menu links to info about the tracks: content, methods

You change the view with pulldown menus

After making changes, REFRESH to enforce the change

enforcechangesEnforcechanges

Change track view

Links to infoand/or filters


Annotation Track Options Defined Hide: removes a track from view

Dense: all items collapsed into a single line

Squish: each item = separate line, but 50% height + packed

Pack: each item separate, but efficiently stacked (full height)

Full: each item on separate line


Mid-page Options to Change Settings

You control the views Use pulldown menus Configure options page

Reset, back to defaults

Start from scratch

Enforce any changes (hide, full, squish…)

Flip display to Genomic 3’5’


Cookies and Sessions

Your browser remembers where you were (cookies)

To clear your “cart” or parameters, click default tracks or reset

OR

Save your setup as “sessions” and store/share them


Click Any Viewer Object for Details

Example: click your mouse anywhere on the TP53 line

Click the item

New description web page opens

Many details and links to more data about TP53


Click Annotation Track Item for Details Pages

Not all genes have this much detail.

Different annotation tracks

carry different data.

informativedescriptionother resource links

microarray data

mRNA secondary structure

links to sequences

protein domains/structure

orthologs in other species

Gene Ontology™ descriptions

mRNA descriptions

pathways

genetic associationstudiescomparative toxicology

gene model


Get DNA, with Extended Case/Color Options Use the DNA link at

the top Plain or Extended

options Change colors,

fonts, etc.


Get Sequence from Details Pages

Click a track, go to Sequence section of details page

Click the item

sequence sectionon detail page


Accessing the BLAT Tool

Rapid searches by INDEXING the entire genome Works best with high similarity matches See documentation and publication for details

Kent, WJ. Genome Res. 2002. 12:656

BLAT = BLAST-like Alignment Tool


BLAT Tool Overview: www.openhelix.com/sampleseqs.html

Make choices

DNA limit 25000 basesProtein limit 10000 aa25 total sequences

Paste one or more

sequences

Or upload

submit


BLAT Results with Hyperlinks

Results with demo sequences, settings default; sort = Query, Score Score is a count of matches—higher number, better match

Click browser to go to Genome Browser image location (next slide) Click details to see the alignment to genomic sequence (2nd slide)

sorting

go

to b

row

ser/

vie

we

r

go

to a

lign

me

nt d

eta

il


BLAT Results: Browser

From browser click in BLAT results A new line with Your Sequence from BLAT Search appears!

Base position = “full” menu and zoomed in enough to see

amino acids in 3 frame translation

query


BLAT Results,Alignment Details

Your query

Genomic match, color cues

Side by Side Alignment

yours

genomic


Introduction Summary

UCSC Genome Browser Visual cues and genomic context Many ways to alter your views Access to deeper data Access and use sequence data

tools in bioinformatics genome browsers. retrieving genomic information previous lesson(s):...

Documents

creditscopyright openhelix

datacopyright openhelix

htmlcopyright openhelix

ucsc genome browserhttp

ucsc genome browser

genome browser gateway

ucsc homepage

creditsbasic searches